SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow_20210722/clean_data/RRBS21T000222_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.2 Cutadapt version: 2.6 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction All Read 2 sequences will be trimmed by 2 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Output file will be GZIP compressed This is cutadapt 2.6 with Python 3.6.7 Command line parameters: -j 1 -e 0.1 -O 1 -a AGATCGGAAGAGC /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow_20210722/tmp/f94f81c0-1990-11ec-9fe6-6c92bfc12faa/trimmed/RRBS21T000222_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 2135.42 s (23 us/read; 2.62 M reads/minute). === Summary === Total reads processed: 93,300,644 Reads with adapters: 57,300,611 (61.4%) Reads written (passing filters): 93,300,644 (100.0%) Total basepairs processed: 9,099,553,356 bp Total written (filtered): 4,125,672,866 bp (45.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 57300611 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 11.5% C: 0.3% G: 66.4% T: 21.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 14386085 23325161.0 0 14386085 2 4350626 5831290.2 0 4350626 3 1730004 1457822.6 0 1730004 4 476000 364455.6 0 476000 5 8278 91113.9 0 8278 6 8813 22778.5 0 8813 7 5560 5694.6 0 5560 8 4140 1423.7 0 4140 9 6169 355.9 0 5375 794 10 7494 89.0 1 2984 4510 11 4987 22.2 1 579 4408 12 1630 5.6 1 252 1378 13 1645 1.4 1 242 1403 14 3710 1.4 1 536 3174 15 2783 1.4 1 460 2323 16 14014 1.4 1 2688 11326 17 25865 1.4 1 10274 15591 18 77631 1.4 1 54681 22950 19 913 1.4 1 301 612 20 2344 1.4 1 529 1815 21 468 1.4 1 260 208 22 1430 1.4 1 780 650 23 2141 1.4 1 393 1748 24 9854 1.4 1 1726 8128 25 3983 1.4 1 615 3368 26 1057 1.4 1 256 801 27 3438 1.4 1 593 2845 28 5824 1.4 1 1052 4772 29 8044 1.4 1 1311 6733 30 2022 1.4 1 378 1644 31 351 1.4 1 30 321 32 2917 1.4 1 465 2452 33 8507 1.4 1 1349 7158 34 7388 1.4 1 1198 6190 35 8763 1.4 1 1177 7586 36 3965 1.4 1 757 3208 37 8099 1.4 1 987 7112 38 10445 1.4 1 2121 8324 39 8073 1.4 1 1608 6465 40 2995 1.4 1 569 2426 41 15688 1.4 1 2957 12731 42 3910 1.4 1 523 3387 43 25273 1.4 1 4569 20704 44 4236 1.4 1 610 3626 45 9989 1.4 1 1900 8089 46 2627 1.4 1 464 2163 47 6139 1.4 1 1039 5100 48 17875 1.4 1 3821 14054 49 1844 1.4 1 288 1556 50 8143 1.4 1 1643 6500 51 3071 1.4 1 649 2422 52 2409 1.4 1 378 2031 53 6393 1.4 1 1047 5346 54 12015 1.4 1 2071 9944 55 14015 1.4 1 2663 11352 56 6945 1.4 1 1171 5774 57 8811 1.4 1 1465 7346 58 5737 1.4 1 1033 4704 59 2373 1.4 1 405 1968 60 4552 1.4 1 790 3762 61 6361 1.4 1 890 5471 62 19032 1.4 1 3194 15838 63 5384 1.4 1 1035 4349 64 1102 1.4 1 200 902 65 586 1.4 1 66 520 66 4023 1.4 1 671 3352 67 2997 1.4 1 377 2620 68 13399 1.4 1 2514 10885 69 15996 1.4 1 2622 13374 70 22752 1.4 1 5249 17503 71 5815 1.4 1 1283 4532 72 3015 1.4 1 594 2421 73 4903 1.4 1 749 4154 74 7562 1.4 1 1075 6487 75 9410 1.4 1 1047 8363 76 11995 1.4 1 1791 10204 77 11815 1.4 1 1943 9872 78 13611 1.4 1 2300 11311 79 29375 1.4 1 4688 24687 80 14297 1.4 1 2215 12082 81 13592 1.4 1 2124 11468 82 14750 1.4 1 2411 12339 83 13114 1.4 1 1446 11668 84 12916 1.4 1 1314 11602 85 14249 1.4 1 1653 12596 86 13340 1.4 1 1708 11632 87 11430 1.4 1 1412 10018 88 11789 1.4 1 1990 9799 89 10280 1.4 1 1343 8937 90 10815 1.4 1 1552 9263 91 13867 1.4 1 2290 11577 92 10593 1.4 1 1544 9049 93 10801 1.4 1 1829 8972 94 12235 1.4 1 1575 10660 95 8530 1.4 1 1295 7235 96 8299 1.4 1 1401 6898 97 9196 1.4 1 1375 7821 98 8657 1.4 1 1336 7321 99 7013 1.4 1 1028 5985 100 6841 1.4 1 976 5865 101 6399 1.4 1 1007 5392 102 6489 1.4 1 1027 5462 103 5702 1.4 1 958 4744 104 5068 1.4 1 774 4294 105 3842 1.4 1 675 3167 106 4026 1.4 1 676 3350 107 4827 1.4 1 764 4063 108 2860 1.4 1 498 2362 109 2383 1.4 1 380 2003 110 2967 1.4 1 508 2459 111 1914 1.4 1 323 1591 112 1345 1.4 1 217 1128 113 111 1.4 1 48 63 114 453 1.4 1 104 349 115 134 1.4 1 64 70 116 307 1.4 1 92 215 117 121 1.4 1 97 24 118 84 1.4 1 64 20 119 88 1.4 1 58 30 120 87 1.4 1 60 27 121 112 1.4 1 86 26 122 122 1.4 1 101 21 123 139 1.4 1 112 27 124 179 1.4 1 148 31 125 192 1.4 1 150 42 126 227 1.4 1 186 41 127 312 1.4 1 247 65 128 390 1.4 1 316 74 129 495 1.4 1 414 81 130 733 1.4 1 616 117 131 962 1.4 1 795 167 132 1536 1.4 1 1269 267 133 3493 1.4 1 2925 568 134 7408 1.4 1 6398 1010 135 9930 1.4 1 8660 1270 136 24903 1.4 1 19718 5185 137 1121928 1.4 1 1086860 35068 138 34271992 1.4 1 33425953 846039 139 80 1.4 1 42 38 140 8 1.4 1 5 3 141 20 1.4 1 13 7 143 6 1.4 1 0 6 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow_20210722/clean_data/RRBS21T000222_val_1.fq.gz ============================================= 93300644 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2109027 (2.3%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 57300572 (61.4%)